reinit the tree, so we can have metadata

5 files changed, 301 insertions, 0 deletions

diff --git a/dev-java/colt/Manifest b/dev-java/colt/Manifest
new file mode 100644
index 000000000000..4f234ceb8a90
--- /dev/null
+++ b/dev-java/colt/Manifest
@@ -0,0 +1,7 @@
+AUX colt-1.2.0-benchmark-no-deprecation.patch 1180 SHA256 822fafff87add40e1d8f29636505713994f23fb30ec20962c3f70ca87b487254 SHA512 523a887bc104062a22ecb4e4350c1c8a4a0be642490b98770943b20e6e8e747d95657d10d042198516b2fd830feb0987ff3473b8ab83278ad3db57d29e9239c7 WHIRLPOOL 4f89d19479c67d85449d052b6cb67edeb6a63f4568ade4685cb1ae3a38810c1c34c4bc08e56f9a346ebeff92576db449061daf16801476aa3d965fb4c87d6e12
+AUX colt-1.2.0-remove-concurrent-util-imports.patch 6924 SHA256 1fb42935dfcbde3383ee73076f86d70a9e639de7e01dca5bf0f83afe8323b23e SHA512 86b568d66b342ede74dc3207268675c8f91b6b3dcc622486d649ba6a0a283de8b20a46f4ac16da8d90d89b4af603b1c8378b990866123e8e4b8b4e3733be4a36 WHIRLPOOL 14c39f22d2199835889c0c4607f9a089b10db01870f7c93c44551c62045eeb08ba6b51f3d59f97867e69ceea642fbc781b3f05e298f6003dc04d8d08ceab7dae
+DIST colt-1.2.0.tar.gz 2545695 SHA256 da26942314a4ab7ab6dc449460970b4ada464b6594f69cba1b88268effbdddbb SHA512 a5e88e0cf671faeb336241d120daeb1ad90f1e2061827d06c0c2dc507cd3ae2ab45f2b80451aaedca0f5a8b3de66c13533178e3b6352ed8b2df886d25a924ce0 WHIRLPOOL 666b49fe22cd40ca3967523a85d1e6b43a7bbbec9f76b197f633e258e2d148b0743308e09f65fc8aad113020477002512f4224d7b412447f0685f2c44f410aad
+EBUILD colt-1.2.0-r3.ebuild 1065 SHA256 896602c12bdc08685b0a2efd397d99008d63d0163120cdd16b0967e3e601ef1e SHA512 aaf5bf0dbb8193ba0b435218d2d23d8cedecfe5812ae65a374525730a2ec36436cd9511bab80e2d77920768231f68bad19cf0159efafb6d72601989c78af016c WHIRLPOOL 67837aafbf7ce9f86109c5e525fbda233468f00e3067adf93f46106c2ddb1d87bb8d3fd606cf32bda0b56c1530168d38d63d78e211dcc1c502103d151e340b00
+MISC ChangeLog 4620 SHA256 7d7ade8cf1e74740490097deb560f9a42780acf535ae6b6b77d6de1fe4a67994 SHA512 5eb045b284e27b786a287b4b782d7aa9c2bc7db1b3653702498928e62cafda0486554f4d62affd38ce5dbc2818bf62a69e1e8a628483d78dae917dd25115c939 WHIRLPOOL 82fde6d64adff29c0ef4adfc358c230d1a59f8b05879d6c95cdcdc78fe8b256be59adf6be9381b12b8b025869e2ef43300a394b74d9a3e1dedb4c87323746cb7
+MISC ChangeLog-2015 3178 SHA256 ebc1b2b5833d46f7202cf01fe3f095b431fd1a9c47334ab74cefbea1d787e079 SHA512 00cb6a54426a5f3b914d1ceb5293fee056066ab32f519a5cd9848c1944336d8d18492c582b7564ad3803fdf5e735a2b3220ef5d887fc80f8fb1533188dd83359 WHIRLPOOL 9f251852f087faf315820c550c01c1a8605ccf7a1d610a5e085ef8e22b1b386812590b6c8081b8e777488f07bdee28e621607cb59203091a06e59c72c151bbe5
+MISC metadata.xml 232 SHA256 0c8d91b3d514ac42d0eaca567346ab909c0f947049c85c25a380ec2400f1b3fb SHA512 00beaf2c81112ff757c4395f4ea47e85f2d48e369e241f10ddf200090dd6513d52ae2b1aef6d28b7417f1cf34608a7258a167eb307d5670323a2190f3710f893 WHIRLPOOL 3a1a6d054edc9177d85ca868f9b0a6e84ee51bab4fbdbb9b1ead1a03874036bcc3f96e903fb751dc4d29fdb7d6b5f3d8dbe7b042fc697c887e23f41cc9c8c4ac
diff --git a/dev-java/colt/colt-1.2.0-r3.ebuild b/dev-java/colt/colt-1.2.0-r3.ebuild
new file mode 100644
index 000000000000..118e1c232f82
--- /dev/null
+++ b/dev-java/colt/colt-1.2.0-r3.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+JAVA_PKG_IUSE="source doc"
+
+inherit java-pkg-2 java-ant-2 eutils
+
+DESCRIPTION="Java Libraries for High Performance Scientific and Technical Computing"
+SRC_URI="http://dsd.lbl.gov/~hoschek/colt-download/releases/${P}.tar.gz"
+HOMEPAGE="http://www-itg.lbl.gov/~hoschek/colt/"
+
+LICENSE="colt"
+IUSE=""
+SLOT="0"
+KEYWORDS="amd64 ~ppc64 x86"
+
+DEPEND=">=virtual/jdk-1.7"
+RDEPEND=">=virtual/jre-1.7"
+
+S="${WORKDIR}/${PN}"
+
+EANT_BUILD_TARGET="javac jar"
+JAVA_ANT_ENCODING="ISO-8859-1"
+
+# [0]: I don't know but it must be useful.
+# [1]: Monkey patch manually some classes to get rid of the
+# oswego.edu.concurrent.util imports.
+PATCHES=(
+	"${FILESDIR}/${P}-benchmark-no-deprecation.patch"
+	"${FILESDIR}/${P}-remove-concurrent-util-imports.patch"
+)
+
+java_prepare() {
+	epatch "${PATCHES[@]}"
+	java-pkg_clean
+}
+
+src_install() {
+	java-pkg_dojar "lib/${PN}.jar"
+
+	dohtml README.html || die
+	use doc && java-pkg_dojavadoc doc/api
+	use source && java-pkg_dosrc src/*
+}
diff --git a/dev-java/colt/files/colt-1.2.0-benchmark-no-deprecation.patch b/dev-java/colt/files/colt-1.2.0-benchmark-no-deprecation.patch
new file mode 100644
index 000000000000..2617dc49ad57
--- /dev/null
+++ b/dev-java/colt/files/colt-1.2.0-benchmark-no-deprecation.patch
@@ -0,0 +1,31 @@
+--- src/cern/colt/matrix/impl/BenchmarkMatrix2D.java	2005-12-13 00:57:28.000000000 -0600
++++ src/cern/colt/matrix/impl/BenchmarkMatrix2D.java	2005-12-13 01:20:09.000000000 -0600
+@@ -331,6 +331,8 @@
+ 	cern.colt.Timer timer1 = new cern.colt.Timer();

+ 	cern.colt.Timer timer2 = new cern.colt.Timer();

+ 

++   cern.jet.math.Functions F = cern.jet.math.Functions.functions;

++

+ 	long size = (((long)rows)*columns)*runs;

+ 

+ 	DoubleMatrix2D  matrix = null;

+@@ -344,7 +346,8 @@
+ 	//if (kind.equals("sparse")) ((SparseDoubleMatrix2D)matrix).elements.hashCollisions = 0;

+ 	for (int i=0; i<runs; i++) {

+ 		timer1.start();

+-		cern.colt.matrix.doublealgo.Transform.mult(matrix, 3);

++		//cern.colt.matrix.doublealgo.Transform.mult(matrix, 3);

++      matrix.assign(F.mult(3));

+ 		timer1.stop();

+ 	}

+ 	timer1.display();

+@@ -366,7 +369,8 @@
+ 	//if (kind.equals("sparse")) ((SparseDoubleMatrix2D)matrix).elements.hashCollisions = 0;

+ 	for (int i=0; i<runs; i++) {

+ 		timer2.start();

+-		cern.colt.matrix.doublealgo.Transform.mult(matrix,3);

++		// cern.colt.matrix.doublealgo.Transform.mult(matrix,3);

++      matrix.assign(F.mult(3));

+ 		timer2.stop();

+ 	}

+ 	timer2.display();

diff --git a/dev-java/colt/files/colt-1.2.0-remove-concurrent-util-imports.patch b/dev-java/colt/files/colt-1.2.0-remove-concurrent-util-imports.patch
new file mode 100644
index 000000000000..2cfbef761baf
--- /dev/null
+++ b/dev-java/colt/files/colt-1.2.0-remove-concurrent-util-imports.patch
@@ -0,0 +1,210 @@
+--- src/cern/colt/matrix/linalg/SmpBlas.java.orig	2015-10-07 22:23:44.969486000 +0000
++++ src/cern/colt/matrix/linalg/SmpBlas.java	2015-10-07 22:29:15.475486000 +0000
+@@ -10,7 +10,8 @@
+ 

+ import cern.colt.matrix.DoubleMatrix1D;

+ import cern.colt.matrix.DoubleMatrix2D;

+-import EDU.oswego.cs.dl.util.concurrent.FJTask;

++

++import java.util.concurrent.ForkJoinTask;

+ /**

+ Parallel implementation of the Basic Linear Algebra System for symmetric multi processing boxes.

+ Currently only a few algorithms are parallelised; the others are fully functional, but run in sequential mode.

+@@ -198,7 +199,7 @@
+ 	

+ 	// set up concurrent tasks

+ 	int span = width/noOfTasks;

+-	final FJTask[] subTasks = new FJTask[noOfTasks];

++	final ForkJoinTask[] subTasks = new ForkJoinTask[noOfTasks];

+ 	for (int i=0; i<noOfTasks; i++) {

+ 		final int offset = i*span;

+ 		if (i==noOfTasks-1) span = width - span*i; // last span may be a bit larger

+@@ -217,24 +218,30 @@
+ 			CC = C.viewPart(offset,0,span,p);

+ 		}

+ 				

+-		subTasks[i] = new FJTask() { 

++		subTasks[i] = new ForkJoinTask() { 

+ 			public void run() { 

+ 				seqBlas.dgemm(transposeA,transposeB,alpha,AA,BB,beta,CC); 

+ 				//System.out.println("Hello "+offset); 

+ 			}

++

++      public boolean exec() { return true; }

++      public void setRawResult(Object o) {}

++      public Object getRawResult() {return null;}

+ 		};

+ 	}

+ 	

+ 	// run tasks and wait for completion

+-	try { 

+-		this.smp.taskGroup.invoke(

+-			new FJTask() {

+-				public void run() {	

+-					coInvoke(subTasks);	

+-				}

+-			}

+-		);

+-	} catch (InterruptedException exc) {}

++  this.smp.taskGroup.invoke(

++          new ForkJoinTask() {

++              public void run() {	

++                  invokeAll(subTasks);	

++              }

++

++              public boolean exec() { return true; }

++              public void setRawResult(Object o) {}

++              public Object getRawResult() {return null;}

++          }

++          );

+ }

+ public void dgemv(final boolean transposeA, final double alpha, DoubleMatrix2D A, final DoubleMatrix1D x, final double beta, DoubleMatrix1D y) {

+ 	/*

+@@ -271,7 +278,7 @@
+ 	

+ 	// set up concurrent tasks

+ 	int span = width/noOfTasks;

+-	final FJTask[] subTasks = new FJTask[noOfTasks];

++	final ForkJoinTask[] subTasks = new ForkJoinTask[noOfTasks];

+ 	for (int i=0; i<noOfTasks; i++) {

+ 		final int offset = i*span;

+ 		if (i==noOfTasks-1) span = width - span*i; // last span may be a bit larger

+@@ -280,24 +287,30 @@
+ 		final DoubleMatrix2D AA = A.viewPart(offset,0,span,n);

+ 		final DoubleMatrix1D yy = y.viewPart(offset,span);

+ 				

+-		subTasks[i] = new FJTask() { 

++		subTasks[i] = new ForkJoinTask() { 

+ 			public void run() { 

+ 				seqBlas.dgemv(transposeA,alpha,AA,x,beta,yy); 

+ 				//System.out.println("Hello "+offset); 

+ 			}

++

++      public boolean exec() { return true; }

++      public void setRawResult(Object o) {}

++      public Object getRawResult() {return null;}

+ 		};

+ 	}

+ 	

+ 	// run tasks and wait for completion

+-	try { 

+-		this.smp.taskGroup.invoke(

+-			new FJTask() {

+-				public void run() {	

+-					coInvoke(subTasks);	

+-				}

+-			}

+-		);

+-	} catch (InterruptedException exc) {}

++  this.smp.taskGroup.invoke(

++          new ForkJoinTask() {

++              public void run() {	

++                  invokeAll(subTasks);	

++              }

++

++              public boolean exec() { return true; }

++              public void setRawResult(Object o) {}

++              public Object getRawResult() {return null;}

++          }

++          );

+ }

+ public void dger(double alpha, DoubleMatrix1D x, DoubleMatrix1D y, DoubleMatrix2D A) {

+ 	seqBlas.dger(alpha,x,y,A);

+@@ -369,9 +382,6 @@
+ /**

+  * Prints various snapshot statistics to System.out; Simply delegates to {@link EDU.oswego.cs.dl.util.concurrent.FJTaskRunnerGroup#stats}.

+  */

+-public void stats() {

+-	if (this.smp!=null) this.smp.stats();

+-}

+ private double xsum(DoubleMatrix2D A) {

+ 	double[] sums = run(A,true,

+ 		new Matrix2DMatrix2DFunction() {

+--- src/cern/colt/matrix/linalg/Smp.java.orig	2015-10-07 21:08:19.443486000 +0000
++++ src/cern/colt/matrix/linalg/Smp.java	2015-10-07 22:28:24.722486000 +0000
+@@ -9,12 +9,13 @@
+ package cern.colt.matrix.linalg;

+ 

+ import cern.colt.matrix.DoubleMatrix2D;

+-import EDU.oswego.cs.dl.util.concurrent.FJTask;

+-import EDU.oswego.cs.dl.util.concurrent.FJTaskRunnerGroup;

++import java.util.concurrent.ForkJoinTask;

++import java.util.concurrent.ForkJoinPool;

++

+ /*

+ */

+ class Smp {

+-	protected FJTaskRunnerGroup taskGroup; // a very efficient and light weight thread pool

++	protected ForkJoinPool taskGroup; // a very efficient and light weight thread pool

+ 

+ 	protected int maxThreads;	

+ /**

+@@ -24,41 +25,39 @@
+ 	maxThreads = Math.max(1,maxThreads);

+ 	this.maxThreads = maxThreads;

+ 	if (maxThreads>1) {

+-		this.taskGroup = new FJTaskRunnerGroup(maxThreads);

++		this.taskGroup = new ForkJoinPool(maxThreads);

+ 	}

+ 	else { // avoid parallel overhead

+ 		this.taskGroup = null;

+ 	}

+ }

+-/**

+- * Clean up deamon threads, if necessary.

+- */

+-public void finalize() {

+-	if (this.taskGroup!=null) this.taskGroup.interruptAll();

+-}

+ protected void run(final DoubleMatrix2D[] blocksA, final DoubleMatrix2D[] blocksB, final double[] results, final Matrix2DMatrix2DFunction function) {

+-	final FJTask[] subTasks = new FJTask[blocksA.length];

++	final ForkJoinTask[] subTasks = new ForkJoinTask[blocksA.length];

+ 	for (int i=0; i<blocksA.length; i++) {

+ 		final int k = i;

+-		subTasks[i] = new FJTask() { 

++		subTasks[i] = new ForkJoinTask() { 

+ 			public void run() {

+ 				double result = function.apply(blocksA[k],blocksB != null ? blocksB[k] : null);

+ 				if (results!=null) results[k] = result; 

+ 				//System.out.print("."); 

+ 			}

++      public boolean exec() { return true; }

++      public void setRawResult(Object o) {}

++      public Object getRawResult() {return null;}

+ 		};

+ 	}

+ 

+ 	// run tasks and wait for completion

+-	try { 

+-		this.taskGroup.invoke(

+-			new FJTask() {

+-				public void run() {	

+-					coInvoke(subTasks);	

+-				}

+-			}

+-		);

+-	} catch (InterruptedException exc) {}

++  this.taskGroup.invoke(

++          new ForkJoinTask() {

++              public void run() {	

++                  invokeAll(subTasks);	

++              }

++              public boolean exec() { return true; }

++              public void setRawResult(Object o) {}

++              public Object getRawResult() {return null;}

++          }

++          );

+ }

+ protected DoubleMatrix2D[] splitBlockedNN(DoubleMatrix2D A, int threshold, long flops) {

+ 	/*

+@@ -186,10 +185,4 @@
+ 	}

+ 	return blocks;

+ }

+-/**

+- * Prints various snapshot statistics to System.out; Simply delegates to {@link EDU.oswego.cs.dl.util.concurrent.FJTaskRunnerGroup#stats}.

+- */

+-public void stats() {

+-	if (this.taskGroup!=null) this.taskGroup.stats();

+-}

+ }

diff --git a/dev-java/colt/metadata.xml b/dev-java/colt/metadata.xml
new file mode 100644
index 000000000000..2444066aa02b
--- /dev/null
+++ b/dev-java/colt/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<maintainer type="project">
+	<email>java@gentoo.org</email>
+	<name>Java</name>
+</maintainer>
+</pkgmetadata>